When comparing WinSCP vs ssh of Windows' Linux subsystem, the Slant community recommends ssh of Windows' Linux subsystem for most people. In the question“What are the best SSH clients for Windows?” ssh of Windows' Linux subsystem is ranked 8th while WinSCP is ranked 12th.
Ranked in these QuestionsQuestion Ranking
Pro Not bundled with Potentially Unwanted Programs (PUP)
Does not attempt to install unwanted software on installation.
Pro Supports FTP and SFTP
In new versions also supports WebDav.
Pro Free and open-source
It has very good compatibility with the other tools of this segment (e.g. PuTTY).
Pro Can protect stored passwords by strong AES cipher
No Installation required.
Pro Can be automated with batch scripts
put a line in bat file ""D:\Program Files\WinSCP\winscp.com" /console /script="D:\ftp\scripts\transfer.txt". All the info can be found on their site.
Pro Integrated basic text editor
It has a integrated basic function text editor to create/edit/update files directly from client.
Pro Already built-in
Pro Based on OpenSSH
OpenSSH is the reference for all ssh clients.
Pro Full Linux shell
Uses all relevant Linux ssh commands as normal.
Pro Excellent way for Windows users to learn Linux
Con Weird keyboard selection handling
If you are accustomed to several commanders, the selection method in WinSCP behaves unexpected - most often selects too much.
Con Keyboard shortcuts not editable
Con Does not support UNC
Does not support UNC. This makes working with the "Library"-function in Win 7, 8, 10 not possible when working over a network.
Con Cut & paste works like the Windows prompt
Con Forces window to a certain size
Any other SSH client will render the remote server at whatever size the local client window is. The built-in SSH client on Windows, however, forces you to use a standard size, and it's small enough to cause problems.